C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy

Maria Doitsidou, Richard J Poole, Sumeet Sarin, Henry Bigelow, Oliver Hobert

Research output: Contribution to journalArticlepeer-review

Abstract

Whole-genome sequencing (WGS) is becoming a fast and cost-effective method to pinpoint molecular lesions in mutagenized genetic model systems, such as Caenorhabditis elegans. As mutagenized strains contain a significant mutational load, it is often still necessary to map mutations to a chromosomal interval to elucidate which of the WGS-identified sequence variants is the phenotype-causing one. We describe here our experience in setting up and testing a simple strategy that incorporates a rapid SNP-based mapping step into the WGS procedure. In this strategy, a mutant retrieved from a genetic screen is crossed with a polymorphic C. elegans strain, individual F2 progeny from this cross is selected for the mutant phenotype, the progeny of these F2 animals are pooled and then whole-genome-sequenced. The density of polymorphic SNP markers is decreased in the region of the phenotype-causing sequence variant and therefore enables its identification in the WGS data. As a proof of principle, we use this strategy to identify the molecular lesion in a mutant strain that produces an excess of dopaminergic neurons. We find that the molecular lesion resides in the Pax-6/Eyeless ortholog vab-3. The strategy described here will further reduce the time between mutant isolation and identification of the molecular lesion.

Original languageEnglish
Pages (from-to)e15435
JournalPLoS ONE
Volume5
Issue number11
DOIs
Publication statusPublished - 2010

Keywords

  • Animals
  • Caenorhabditis elegans
  • Caenorhabditis elegans Proteins
  • Chromosome Mapping
  • Female
  • Genetic Association Studies
  • Genome, Helminth
  • Genome-Wide Association Study
  • Genotype
  • Male
  • Mutation
  • Paired Box Transcription Factors
  • Phenotype
  • Polymorphism, Single Nucleotide
  • RNA Interference
  • Reproducibility of Results
  • Sequence Analysis, DNA
  • Software

Fingerprint

Dive into the research topics of 'C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy'. Together they form a unique fingerprint.

Cite this